The metagenomic approach and causality in virology

Castrignano, Silvana Beres; Nagasse-Sugahara, Teresa Keico

The need to identify the correct host and the potential pathogenicity of the virus is also imperative when a previously unknown virus is found in fecal samples or upper respiratory tract secretions. The presence of a virus in these samples during the acute phase of the disease does not necessarily make this agent responsible for the pathology. This can be the case when a virus shedded from the host for a prolonged period, e.g., enterovirus and bocavirus, is detected. 29 In addition, a virus detected in fecal samples or respiratory tract secretions may have been inhaled or ingested and may have passed through the lumen of the respiratory or digestive tract without replicating into that host. 3, 12 The human bocavirus exemplifies the difficulty in evaluating the causal association between a newly discovered virus in the respiratory tract and the clinical manifestations. Bocaviruses were discovered in 2005 using a metagenomic approach in a pool of randomly selected samples of nasopharyngeal aspirates 1 and have been a topic of intense research since then. This research has indicated that the factors that hinder the establishment of a causal association between the virus and disease include the high prevalence of bocavirus infection, prolonged viral shedding by the host after infection, persistence of the viral DNA in the respiratory tract for several months, and high rate of coinfection. The studies conducted to date suggest that bocaviruses are sometimes transient passengers and eventually pathogens of the respiratory tract. 4, 29 Even when the metagenomic approach leads to the detection of a new virus in the cerebrospinal fluid (CSF), which is generally sterile, the disease cannot be associated with the virus before further investigation. 26 This hypothesis can be discussed on the basis of recent findings of Tan et al, 26 who found a new cyclovirus in CSF specimens of two patients with an acute infection of the central nervous system. After its identification, this virus was detected in 4.0% of 642 CSF samples from patients suspected of having an infection of the central nervous system; however, it was not detected in any of the 122 samples from patients with a noninfectious neurologic disease. The viral genome was also found in fecal samples of healthy children, which suggested food-borne or fecal-oral transmission route. In addition, it was found in animal feces, suggesting the existence of animal reservoirs for this virus. These authors affirmed that, considering the current knowledge, it is impossible to establish a causal association between this virus and the disease according to Koch's criteria or their adapted versions. For further assessment of this association, Tan et al 26 are attempting to isolate the virus in cell cultures or animal models and to detect a specific immune response. This is a justifiable caution because a virus found in CSF can be a coinfectious agent -which would play a secondary role in disease pathology and could increase disease severity or facilitate the entry of other pathogens -, or a latent virus that was reactivated because of an infectious/inflammatory process, or it can simply reflect the detection of a latent virus. 6, 22, 23, 26 This discussion is common in cases of detection in CSF of human herpesviruses that are disseminated through the hematogenous route, such as the Epstein-Barr virus and the human herpesvirus 6. 6, 22, 23 The new cyclovirus could also be like the anelloviruses, which establis